Rpd3S in complex with 187bp nucleosome
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 8kd2
Q-score: 0.35
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Linker tightening state of rpd3s-ncp(187bp) (Complex)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8kd3
Q-score: 0.376
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- H3k9 deacetylation state of rpd3s-ncp (187bp/mla/k9q) (Complex)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8kd4
Q-score: 0.373
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla)class1 (Complex)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Rpd3-sin3-rco1-eaf3 (Complex from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8kd5
Q-score: 0.378
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (Complex from synthetic construct)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp (187bp/mla) class2 (Complex)
- Histone (Complex from Xenopus laevis)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8kd6
Q-score: 0.311
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla) class3 (Complex)
- Dna (Complex)
Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 8kd7
Q-score: 0.324
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- 167bp dna (51 kDa, DNA from synthetic construct)
- Eaf3-rpd3-sin3 (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Alternative deacetylation state of rpd3s-ncp(167bp/mla) (Complex)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 167bp dna (51 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- 167bp dna (Complex from synthetic construct)
- Histone (Complex from Xenopus laevis)
Cryo-EM map of Eaf3 CHD bound to H3K36me3 nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7yi1
Q-score: 0.572
Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H
Nature (2023) 620 pp. 669-675 [ DOI: doi:10.1038/s41586-023-06349-1 Pubmed: 37468628 ]
- Eaf3 (Complex from Xenopus laevis)
- Dna (Complex from Saccharomyces cerevisiae S288C)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4/h2a/h2b 1.1 (Complex from synthetic construct)
- Histone h3 (Complex)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Cryo-EM map of Rpd3S complex bound to H3K36me3 nucleosome in close state
Resolution: 3.96 Å
EM Method: Single-particle
Fitted PDBs: 7yi4
Q-score: 0.23
Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H
Nature (2023) 620 pp. 669-675 [ DOI: doi:10.1038/s41586-023-06349-1 Pubmed: 37468628 ]
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (Complex from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h4/h2a/h2b 1.1 (Complex from synthetic construct)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Histone h3 (Complex)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Sin3/rpd3/eaf3/rco1 (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae S288C)
Cryo-EM msp of Rpd3S complex bound to H3K36me3 nucleosome in loose state
Resolution: 3.96 Å
EM Method: Single-particle
Fitted PDBs: 7yi5
Q-score: 0.254
Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H
Nature (2023) 620 pp. 669-675 [ DOI: doi:10.1038/s41586-023-06349-1 Pubmed: 37468628 ]
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (Complex from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h4/h2a/h2b 1.1 (Complex from synthetic construct)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Histone h3 (Complex)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Sin3/rpd3/eaf3/rco1 (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae S288C)